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As Linux celebrates its 20th birthday, its biggest success – mobile – is turning into its worst headache.

Thanks to Google's Android, and in turn thanks to the success of Steve Jobs' iPhone and iPad, Linux has found a fresh lease of life.

Smartphones running the Android version of Linux account for 39 per cent of the market; Android has given existing phone-makers a fresh opportunity and propelled newcomers. iOS is second to Android on 29 per cent of the smartphone market, coming as it does from just a single OEM: Apple. iOS is number-one on tablets, however, with Android coming second.

The smartphone and tablet have arrived just as it seemed Linux's biggest disruptive days were behind it.

What started as an off-the-radar hobby for geeks had crossed into the business mainstream by the 2000s as companies recognised it as an alternative to the cost and lock-in of Windows on the server.

While Linux failed to unlock the desktop, still owned by Windows, it was application and server makers' adoption of it that turned Linux into the second most popular server operating system. Linux has borne various distros running on those servers – Red Hat, SuSE and Ubuntu being the most popular.

And yet, Linux is second, not first – albeit a healthy second. Despite the hard work by IBM, HP and Dell in making and selling servers, and the engineering and support work of Red Hat, Novell and Canonical, Linux still lags Windows.

Linux ascended despite the best efforts of Microsoft to discredit and sabotage it. Microsoft called Linux a "cancer" that threatened software makers' IP, it launched a "get the facts" campaign to undermine the commercial story for Linux, and tried to put people off by insinuating they risked prosecution by Microsoft as Linux contained Microsoft patents.

Microsoft's attacks blew themselves out, though, and cooler business heads are in charge as Microsoft's server business has worked to make Linux run better on Windows server through its hypervisor software. Linux on the Windows hypervisor means more Windows servers in the cloud, rather than Windows servers losing out to Linux servers in the cloud.

Microsoft hasn't stopped being any less threatening towards Linux, however, it has just changed tactics as the excitement shifts to mobile. As phone sales have exploded, Redmond has started hunting down Android device-makers, claiming the Linux they love violates its patents, and it is either prosecuting them or tying them up in deals to license its patent portfolio. The result is that Microsoft is profiting from Android, because under these deals Microsoft gets a percentage of the money from the sale of each Android phone.

Microsoft's attacks have come as Apple has turned aggressively litigious against Android and those companies making and selling phones and tablets running Linux.

Round up the cheerleaders

As the heat is turning up, the company responsible for Android – and credited for having propelled Linux into mobile – has taken two steps that have left techs speechless. The standing army of cheerleaders who've spent the last few years shouting about how it's game over for Apple, Microsoft, Nokia, RIM and anybody else not in love with Android are suddenly chilled by uncertainty.

First, Google caused consternation by ending the Android code free-for-all. It broke with its practice of open-sourcing the most recent version of Android – Honeycomb. Google claimed it took a "shortcut" to get Honeycomb to market and did not release the code because it was not suited for use on phones. The next version of Android, dubbed "Ice Cream Sandwich", will be open-sourced "by the end of the year", we are now told.

Next, Google unsettled Android OEM partners with its plan to spend $12.5bn buying Motorola's phone business – Motorola being the world's second-largest maker of Android handsets. Google's Android chief Andy Rubin claims it's business as usual and that Google's Android partners are on board with the deal, but the facts say otherwise.